Difference between revisions of "Documentation/Nightly/Modules/AirwaySegmentation"

From Slicer Wiki
Jump to: navigation, search
(Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…')
 
m (Updating contributor's emails)
(39 intermediate revisions by the same user not shown)
Line 9: Line 9:
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
Extension: [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]]<br>
 
Extension: [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]]<br>
−
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
+
Acknowledgments:
−
Author: Pietro Nardelli, University College Cork<br>
+
This work is supported by NA-MIC, the Slicer Community and University College of Cork.<br>
−
Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br>
+
Author: Pietro Nardelli (University College Cork)<br>
−
Contact: Pietro Nardelli, <email>111126418@umail.ucc.ie</email><br>
+
Contributor1:<br>
 +
Contact: Pietro Nardelli, <email>pnardelli@bwh.harvard.edu</email>, <email>pie.nardelli@gmail.com</email><br>
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
 
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
−
|{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}} <- Replace this logo with yours
+
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
−
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}   <-Replace this logo with yours
+
|Image:UCC-logoNEW.png|University College Cork (UCC)
 +
|Image:Biolectromagnetics_group_UCC.jpg|Bioelectromagnetics group UCC
 +
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
 
}}
 
}}
 +
 
{{documentation/{{documentation/version}}/module-introduction-end}}
 
{{documentation/{{documentation/version}}/module-introduction-end}}
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Module Description}}
 
{{documentation/{{documentation/version}}/module-section|Module Description}}
−
N/A
+
AirwaySegmentation is an extension for airway segmentation starting from chest CT images. Two modules come with this extension. A simple CLI module, called Airway Segmentation CLI, that uses a modified version of ITK's itkConnectedThresholdImageFilter to segment all the pixels with an intensity below a threshold. The threshold is automatically identified by the module. To use this module for the segmentation, the user is required to place only one
−
<!--
+
fiducial point within the trachea. This fiducial is used as starting point for the region growing segmentation. Also, using this module, the user needs to specify the convolution kernel used for reconstructing the DICOM image. A scripted module, called AirwaySegmentation, is also available. This is a python module that automatically invokes the CLI module described above. It automatically extracts the convolution kernel of the image, and for this reason it only works for DICOM images. The output volume is also automatically created. This way, the user needs to only specify the input volume, and the fiducial placed in the trachea. A label color can also be optionally selected.
−
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
 
−
 
 
−
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}
 
−
 
 
−
{{documentation/{{documentation/version}}/module-description}}
 
−
-->
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
{{documentation/{{documentation/version}}/module-section|Use Cases}}
−
N/A
+
*Airway Segmentation starting from chest CT datasets
 +
 
 +
{|
 +
|[[Image:Screenshot from 2015-01-08 11-32-48.jpg|thumb|500px|Airway Segmentation Scripted Module: example of usage]]
 +
|}
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Tutorials}}
 
{{documentation/{{documentation/version}}/module-section|Tutorials}}
 +
 
N/A
 
N/A
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
−
N/A
+
 
−
<!--
+
* <span>'''''IO Parameters'''''</span>: Input and Output parameters.
−
{{documentation/{{documentation/version}}/module-parametersdescription}}
+
** <span>'''Input Volume'''</span>: Input chest CT dataset to be segmented.
−
-->
+
** <span>'''Seed'''</span>: Seed point for the algorithm. Only one seed point must be placed within the trachea. If using an pig CT chest image, the fiducial has to be placed between the carina and the further branch coming out of the trachea.
 +
 
 +
* <span>'''''Segmentation Parameters'''''</span>: Input parameters for segmentation (optional).
 +
** <span>'''Airway Label Color'''</span>: The integer value (0-255) to use for the segmentation results. This will determine the color of the segmentation that will be generated by the algorithm.
 +
The user interface panel for the scripted module:
 +
 
 +
{|
 +
|[[Image:AirwaySegmentation_Scripted_Interface.jpg|thumb|300px|{{documentation/modulename}} Scripted Module Interface ]]
 +
|}
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
Line 52: Line 63:
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|References}}
 
{{documentation/{{documentation/version}}/module-section|References}}
−
N/A
+
Nardelli, P., Khan, K. A., Corvò, A., Moore, N., Murphy, M. J., Twomey, M.,  O’Connor, O. J., Kennedy, M. P., Estépar, R. S. J., Maher, M. M. & Cantillon-Murphy, P. (2015). Optimizing parameters of an open-source airway segmentation algorithm using different CT images. Biomedical engineering online, 14(1), 62.
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
−
{{documentation/{{documentation/version}}/module-developerinfo}}
+
The code is available at [https://github.com/PietroNardelli/Slicer-AirwaySegmentation Github].
−
 
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-footer}}
 
{{documentation/{{documentation/version}}/module-footer}}
 +
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->

Revision as of 09:29, 3 January 2018

Home < Documentation < Nightly < Modules < AirwaySegmentation


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

Extension: AirwaySegmentation
Acknowledgments: This work is supported by NA-MIC, the Slicer Community and University College of Cork.
Author: Pietro Nardelli (University College Cork)
Contributor1:
Contact: Pietro Nardelli, <email>pnardelli@bwh.harvard.edu</email>, <email>pie.nardelli@gmail.com</email>

National Alliance for Medical Image Computing (NA-MIC)  
University College Cork (UCC)  
Bioelectromagnetics group UCC  
Surgical Planning Laboratory (SPL)  

Module Description

AirwaySegmentation is an extension for airway segmentation starting from chest CT images. Two modules come with this extension. A simple CLI module, called Airway Segmentation CLI, that uses a modified version of ITK's itkConnectedThresholdImageFilter to segment all the pixels with an intensity below a threshold. The threshold is automatically identified by the module. To use this module for the segmentation, the user is required to place only one fiducial point within the trachea. This fiducial is used as starting point for the region growing segmentation. Also, using this module, the user needs to specify the convolution kernel used for reconstructing the DICOM image. A scripted module, called AirwaySegmentation, is also available. This is a python module that automatically invokes the CLI module described above. It automatically extracts the convolution kernel of the image, and for this reason it only works for DICOM images. The output volume is also automatically created. This way, the user needs to only specify the input volume, and the fiducial placed in the trachea. A label color can also be optionally selected.

Use Cases

  • Airway Segmentation starting from chest CT datasets
Airway Segmentation Scripted Module: example of usage

Tutorials

N/A

Panels and their use

  • IO Parameters: Input and Output parameters.
    • Input Volume: Input chest CT dataset to be segmented.
    • Seed: Seed point for the algorithm. Only one seed point must be placed within the trachea. If using an pig CT chest image, the fiducial has to be placed between the carina and the further branch coming out of the trachea.
  • Segmentation Parameters: Input parameters for segmentation (optional).
    • Airway Label Color: The integer value (0-255) to use for the segmentation results. This will determine the color of the segmentation that will be generated by the algorithm.

The user interface panel for the scripted module:

AirwaySegmentation Scripted Module Interface

Similar Modules

N/A

References

Nardelli, P., Khan, K. A., Corvò, A., Moore, N., Murphy, M. J., Twomey, M., O’Connor, O. J., Kennedy, M. P., Estépar, R. S. J., Maher, M. M. & Cantillon-Murphy, P. (2015). Optimizing parameters of an open-source airway segmentation algorithm using different CT images. Biomedical engineering online, 14(1), 62.

Information for Developers

The code is available at Github.

Retrieved from "https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/AirwaySegmentation&oldid=57607"